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Yorodumi- PDB-1uhn: The crystal structure of the calcium binding protein AtCBL2 from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uhn | ||||||
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Title | The crystal structure of the calcium binding protein AtCBL2 from Arabidopsis thaliana | ||||||
Components | calcineurin B-like protein 2 | ||||||
Keywords | METAL BINDING PROTEIN / calcium binding protein | ||||||
Function / homology | Function and homology information plant-type vacuole membrane / potassium ion homeostasis / plant-type vacuole / vacuole / plastid / cytosolic ribosome / calcium-mediated signaling / kinase binding / calcium ion binding / membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å | ||||||
Authors | Nagae, M. / Nozawa, A. / Koizumi, N. / Sano, H. / Hashimoto, H. / Sato, M. / Shimizu, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The Crystal Structure of the Novel Calcium-binding Protein AtCBL2 from Arabidopsis thaliana Authors: Nagae, M. / Nozawa, A. / Koizumi, N. / Sano, H. / Hashimoto, H. / Sato, M. / Shimizu, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uhn.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uhn.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 1uhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/1uhn ftp://data.pdbj.org/pub/pdb/validation_reports/uh/1uhn | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21907.898 Da / Num. of mol.: 1 / Fragment: residues 32-220 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)SI / References: UniProt: Q8LAS7 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 51.97 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 8000, lithium chloride, MES, calcium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Nagae, M., (2003) Acta Crystallogr., D59, 1079. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 28, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.9 Å / Num. all: 14399 / Num. obs: 14399 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 1.9 / Num. unique all: 7568 / % possible all: 96.3 |
Reflection | *PLUS Num. measured all: 80068 |
Reflection shell | *PLUS % possible obs: 96.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→39.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→39.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å /
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Refinement | *PLUS Lowest resolution: 35.58 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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